Ok, after starting to look into another bug report (duplication-related), I've discovered that it might be possible to completely do away with the placeholder ghosts. Since version 1.1.86, players can copy (and maybe cut) a friendly force's ghosts/blueprints.
However... This is not the case with deconstruction planner - that is, you will not get visual indication that you have selected the allied force's ghost entities. Although, due to the way deconstruction is handled by the mod, it will still work correctly (minus the already present caveat of not supporting game/player library deconstruction plans).
On the other hand... The deconstruction planner is effectively selecting just the ticks, which is only half-helpful. You get an idea of how many unapproved ghosts will get removed, but not also what they are.
So... At least for the first next release, I'll keep all the boxes ticked (pun intended), but maybe down the line I will revisit this. Perhaps one solution would be to provide both variants via configuration. No promises made, though :)
As for your suggestion on placing the placeholder as an entity... Looks like I've already left a comment for myself in the code back in the day :)
-- The placeholder has to be a ghost, otherwise it will overwrite the unapproved entity, and mess up the
-- deconstruction planner interaction
So... That's a no-no, unfortunately (deconstruction planner interaction refers to some undo black magic as well).
Best regards,
Branko